Extracting k-mer counts from multiple genome sequence files
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18 months ago
yas ▴ 20

Good day everyone, I am new here.

So, I have downloaded 8 completed genome fasta files for 8 strains of Bacillus subtilis spp.

My aim is to do classification based on their k-mer abundance profiles.

I am wondering, is there any tools that I can use to generate and extract the k-mer counts for each of the 8 genome files in a single output?

k-mer • 1.2k views
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17 months ago

Two very popular tools specifically designed for k-mer counting:

  1. KMC3 [tool] [paper]

  2. Jellyfish [tool] [paper]

Other k-mer counting tools are listed in the benchmark study of k-mer counting methods.

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Thank you!

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18 months ago
5heikki 11k

Mash is an excellent tool for this kind of thing. It's far more sophisticated than simple k-mer abundance counting..

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Thank you so much for the answer. But I need to generate the k-mer abundance profiles.

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18 months ago

You could use kmercountmulti.sh from the BBTools Suite if you are specifically interested in k-mers.

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Thanks for the suggestion.

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